Background Larval source management is a promising component of integrated malaria control and elimination. This requires development of a framework to target productive locations through process-based understanding of habitat hydrology and geomorphology. Methods We conducted the first catchment scale study of fine resolution spatial and temporal variation in Anopheles habitat and productivity in relation to rainfall, hydrology and geomorphology for a high malaria transmission area of Tanzania. Results Monthly aggregates of rainfall, river stage and water table were not significantly related to the abundance of vector larvae. However, these metrics showed strong explanatory power to predict mosquito larval abundances after stratification by water body type, with a clear seasonal trend for each, defined on the basis of its geomorphological setting and origin. Conclusion Hydrological and geomorphological processes governing the availability and productivity of Anopheles breeding habitat need to be understood at the local scale for which larval source management is implemented in order to effectively target larval source interventions. Mapping and monitoring these processes is a well-established practice providing a tractable way forward for developing important malaria management tools.