Shouldn't Structural Engineer have known about the water table?

We recently redid the foundation of our small house in Berkeley, replacing the crumbling original foundation which was more than 100 years old. We hired a structural engineer who suggested we could also expand a small storage area under the house. The structural engineer made plans for the foundation and a larger storage area. We hired a contractor based on those plans. As the contractor dug out what would be the storage area, there was constant water. We had to make the storage area smaller than in the plans because it kept flooding. The storage area that we got in the end is deeper than what was there before. We now have a sub-pump routinely clunking in the night. I feel that we paid for a larger storage area than we got. Shouldn't the structural engineer have been able to foresee the issue with the water table? 

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No a structural engineer wouldn't have known about this. Groundwater is more of a geotechnical 'problem'. Typically they would be the one to determine groundwater levels and provide guidance for the foundation design and construction. Groundwater levels can fluctuate throughout the year and there might be localized areas of high groundwater as well. Most residential projects don't pay for geotechnical studies to be done. There are construction dewatering methods that can be used it mitigate groundwater (such as using pumps to keep the water low).

Retired architect chiming in here. Structural engineers are not geotechnical engineers. In other words, soils and water tables are not under a structural engineer's purview. If you did not contract with a geotechnical engineer to have a geotechnical study and report done for the property and provide the information to the structural engineer, the structural engineer would not have had that information when designing the foundation. I would have expected the city to require a geotechnical report for the type of work you describe.