5 Best ETL Tools for ClickHouse Integration (2025 Guide)

ClickHouse is one of the most widely adopted real-time analytical databases, valued for its high performance, scalability, and ability to handle massive amounts of data efficiently. It is often used to power analytics dashboards, process event streams, and support machine learning workloads.

To fully unlock the potential of ClickHouse, you need an effective way to bring data into it. That is where ETL tools for ClickHouse integration play an important role. These tools make it possible to extract data from source systems, apply transformations, and load it into ClickHouse for analysis.

In 2025, the landscape of ETL tools is evolving. Some solutions focus on batch data loading, while others provide streaming-first capabilities that deliver real-time insights. Choosing the right tool depends on your business needs, technical resources, and budget.

This article explores the five best ETL tools for ClickHouse integration. We will review each option, including Estuary Flow, Airbyte, Fivetran, Debezium with Kafka, and Apache Airflow, so you can make an informed decision about which approach works best for your organization.

Why ETL Tools Matter for ClickHouse

ClickHouse is designed to process queries at lightning speed, but the performance of your analytics stack depends on how efficiently you can move data into it. Without a reliable pipeline, even the fastest database can fall short. This is where ETL tools for ClickHouse become essential.

Key Use Cases for ClickHouse ETL

• Real-time analytics dashboards: Keeping dashboards updated with the latest data from sources like PostgreSQL, MySQL, or SaaS applications.
• Event stream processing: Ingesting logs, IoT events, or clickstream data for immediate insights.
• Customer 360 views: Combining multiple systems such as CRM, ERP, and web analytics into a single source of truth in ClickHouse.
• Machine learning feature stores: Delivering continuous data feeds into ClickHouse so ML models have fresh, reliable training data.

Challenges of DIY Pipelines

While it is technically possible to build custom pipelines with scripts or direct APIs, this approach quickly runs into challenges:

• Handling schema drift when data structures change.
• Ensuring exactly-once delivery to prevent duplicates or data loss.
• Scaling infrastructure to handle large volumes of streaming data.
• Managing ongoing monitoring, error handling, and maintenance.

The Role of ETL Tools

Modern ClickHouse integration tools remove these obstacles by offering pre-built connectors, real-time streaming capabilities, and automated error handling. They allow teams to focus on deriving insights rather than managing data plumbing. In 2025, the difference often comes down to whether you choose a batch-first tool or a streaming-first platform, depending on your need for data freshness.

Want a hands-on look? Try Estuary Flow free → and see how real-time ETL pipelines into ClickHouse work in minutes.

Best ETL Tools for ClickHouse Integration

If you are exploring ways to stream or load data into ClickHouse, the right ETL solution can simplify the process and ensure reliable performance. Below are five of the most effective tools for integrating data with ClickHouse, each offering different approaches depending on your requirements.

1. Estuary Flow

Estuary Flow is a real-time ETL and data streaming platform that makes it simple to move data from operational databases, SaaS applications, and event streams into ClickHouse. Unlike batch-first tools, Flow is designed to deliver continuous updates with exactly-once delivery and schema enforcement, ensuring your ClickHouse instance is always synchronized and analytics-ready.

Flow supports Change Data Capture (CDC) from databases such as PostgreSQL, MySQL, and MongoDB, as well as a wide variety of SaaS and event sources. With its ClickHouse integration powered by the Dekaf connector, Flow materializes data as Kafka-compatible messages that ClickHouse can consume through ClickPipes.

Key Benefits of Using Estuary Flow with ClickHouse

• Real-time streaming: Keep your ClickHouse tables updated continuously, not in delayed batches.
• Exactly-once delivery: Prevent duplicate records or missing data.
• Schema enforcement: Ensure compatibility between source systems and ClickHouse.
• No-code setup: Build production pipelines without writing custom code.
• Flexible deployment: Available as SaaS, private deployment, or bring-your-own-cloud.

Ready to build your first pipeline? Start streaming data into ClickHouse with Estuary Flow today →

2. Airbyte

Airbyte is a widely used open-source ETL and ELT platform that provides connectors for hundreds of data sources and destinations, including ClickHouse. It is a popular choice for teams that want a community-driven solution with flexibility to customize pipelines.

Airbyte supports both self-hosted deployments and a fully managed cloud service, making it accessible for startups as well as enterprises. The ClickHouse connector allows you to load data from databases, APIs, and SaaS platforms directly into ClickHouse tables.

Key Benefits of Using Airbyte with ClickHouse

• Open-source: Full transparency and the ability to extend or modify connectors.
• Wide connector ecosystem: Hundreds of source connectors maintained by Airbyte and its community.
• Hybrid deployment options: Choose between Airbyte Cloud or running it on your own infrastructure.

Limitations

• Primarily batch-based, so it may not deliver real-time updates into ClickHouse.
• Requires ongoing infrastructure management if self-hosted.
• Scaling large pipelines can add complexity and costs.

3. Fivetran

Fivetran is a fully managed ETL and ELT platform designed for enterprises that want reliable data pipelines without managing infrastructure. It is known for its automation, ease of use, and strong ecosystem of pre-built connectors.

While Fivetran does not offer a native ClickHouse connector in its core product, ClickHouse integrations are available through partner and community connectors. This makes it possible to move data from popular sources such as Salesforce, Oracle, or PostgreSQL into ClickHouse.

Key Benefits of Using Fivetran with ClickHouse

• Enterprise-grade reliability: Automated schema management and monitoring.
• Hands-off operation: Minimal engineering required once pipelines are configured.
• Broad connector coverage: Hundreds of sources supported across databases, SaaS apps, and APIs.

Limitations

• High cost due to its Monthly Active Rows (MAR)-based pricing model, which can scale quickly as data volumes grow.
• Pipelines are primarily batch-oriented, not streaming-first.
• Direct ClickHouse support is limited and may require workarounds compared to destinations like Snowflake or BigQuery.

4. Debezium + Kafka + ClickHouse

For engineering teams that prefer a fully open-source and customizable stack, combining Debezium with Apache Kafka and the ClickHouse Kafka sink is a powerful option.

Debezium is an open-source platform for Change Data Capture (CDC). It can stream database changes from systems like PostgreSQL, MySQL, and SQL Server into Kafka topics. From there, ClickHouse can consume the Kafka streams through its built-in Kafka engine or via ClickPipes in ClickHouse Cloud.

Key Benefits of Using Debezium + Kafka with ClickHouse

• Streaming-first architecture: Provides near real-time ingestion of database changes.
• High flexibility: Fully customizable pipelines tailored to specific business needs.
• Open-source: No vendor lock-in, supported by a strong community.

Limitations

• Requires significant engineering resources to deploy, manage, and monitor.
• Complexity increases when handling schema evolution, retries, and exactly-once semantics.
• Best suited for teams already experienced with Kafka.

5. Apache Airflow

Apache Airflow is an open-source workflow orchestration platform widely used for building and scheduling data pipelines. While Airflow is not an ETL tool by itself, it can be used to orchestrate ETL jobs that move and transform data into ClickHouse.

With its Python-based framework, Airflow allows you to create Directed Acyclic Graphs (DAGs) that define how data should flow between systems. For ClickHouse integration, Airflow can run custom scripts or operators that extract data from sources, apply transformations, and load results into ClickHouse tables.

Key Benefits of Using Airflow with ClickHouse

• Highly flexible: Full control over pipeline logic and scheduling.
• Extensible: Rich ecosystem of operators and plugins, plus the ability to write custom integrations.
• Proven orchestration tool: Widely adopted in modern data engineering workflows.

Limitations

• Airflow itself is not real-time. It works best for batch jobs and scheduled workflows.
• Requires engineering resources to maintain infrastructure and ensure reliability.
• No built-in ClickHouse connector, so integration often relies on custom scripts or third-party operators.

Not sure which tool suits your needs? Contact us and our team can help you map the right path for your ClickHouse ETL setup.

Comparison of ETL Tools for ClickHouse

See how Estuary stacks up to other tools: Estuary vs Airbyte - transparent pricing, real-time support, zero fuss.

How to load data into ClickHouse in Minutes

Step 1: Prerequisites

• At least one Flow collection created in Estuary.
• A ClickHouse Cloud account with permissions to configure ClickPipes.

Step 2: Create a Dekaf Materialization in Flow

• In Estuary Flow, configure a Dekaf materialization with the clickhouse variant.
• Provide an Auth Token (your chosen password for authentication).
• Note the full materialization name (for example: ORG/PREFIX/MATERIALIZATION). This will be your username when connecting.

Step 3: Configure ClickPipes in ClickHouse Cloud

• Navigate to Integrations and select Apache Kafka as the data source.
• Enter the following connection parameters:
  • Broker Address: dekaf.estuary-data.com:9092
  • Schema Registry: https://dekaf.estuary-data.com
  • Security Protocol: SASL_SSL
  • SASL Mechanism: PLAIN
  • SASL Username: your full materialization name
  • SASL Password: the Auth Token you specified
  • Schema Registry Username: same as SASL username
  • Schema Registry Password: same as SASL password

Step 4: Map Data Fields

• Use ClickHouse’s mapping interface to align Flow collection fields with ClickHouse table columns.

Step 5: Provision the ClickPipe

• Start the integration. ClickPipes will set up the pipeline within seconds, and Estuary Flow will begin streaming data into ClickHouse in real time.

For full technical detail, view the ClickHouse connector documentation

Key Takeaways

• ClickHouse requires reliable ETL tools to unlock its full power for analytics, event processing, and machine learning.
• Estuary Flow stands out with real-time, exactly-once, and no-code pipelines, making it the most balanced choice for ClickHouse integration.
• Airbyte is a flexible, open-source option, but it is primarily batch-based.
• Fivetran offers enterprise reliability, though it comes with high costs and limited real-time support.
• Debezium + Kafka provides real-time CDC pipelines but demands strong engineering resources.
• Apache Airflow is best for orchestration and batch workflows rather than continuous ETL.

If you need to stream data into ClickHouse in real time with minimal effort, Estuary Flow is the most effective solution to consider.

Conclusion

Whether you prefer open-source flexibility, fully managed enterprise services, or modern streaming-first platforms, these ETL tools provide multiple ways to integrate data into ClickHouse easily. The best choice depends on your workload, budget, and technical expertise. For most modern use cases where real-time analytics and continuous data pipelines are essential, Estuary Flow offers the fastest and most reliable path to production pipelines.

Join companies already moving faster with Estuary: Read our success stories or Register now to get started.