Many real-world data science tasks involve complex web-based interactions: finding appropriate data available on the internet, synthesizing multimodal data from different locations, and producing summarized analyses. Existing web benchmarks often focus on simplistic interactions and often do not require diverse tool-using capabilities. Conversely, traditional data science benchmarks typically concentrate on static, highly structured datasets and do not assess end-to-end workflows that encompass data acquisition, cleaning, analysis, and insight generation. In response, we introduce WebDS, the first end-to-end web-based data science benchmark. It comprises 870 web-based data science tasks across 29 diverse websites from structured government data portals to unstructured news media, challenging agents to perform complex, multi-step, tool-based operations, across heterogeneous data formats, to better reflect the realities of modern data analytics. Evaluations of current SOTA LLM agents indicate significant performance gaps in accomplishing these tasks. For instance, Browser Use, which accomplishes $80\%$ of tasks on WebVoyager, completes only 15% of tasks in WebDS, which our analysis suggests is due to new failure modes, such as poor information grounding, repetitive behavior and shortcut-taking that agents performing WebDS's tasks display. By contrast, humans achieve around 90% accuracy, highlighting a substantial gap between current agents and human performance. By providing a more robust and realistic testing ground, WebDS sets the stage for significant advances in the development of practically useful LLM-based data science.