Groundwater dynamics affect lake water budgets, but its major factors and mechanisms still need clarification. This study evaluates the effects of surrounding groundwater flow on seepage direction and assesses factors that affect seepage flux in a closed-basin lake in northeastern Estonia – Lake Martiska. A piezometric map was used to determine directions of groundwater flow around the lake. Seepage meters were applied for measuring flux at 44 locations along eight transects in the lake in relation to water depth, distance from the shore, sediment type and thickness of organic sediment. Additionally nearshore ice-free areas were mapped in winter. Seepage patterns followed the estimated directions of groundwater flow in nearshore areas. Outseepage records showed the impacts of nearby groundwater-abstraction wells on groundwater flow. However, the within-lake seepage direction and flux differed from the expected at 6–15 m from the shore and water depth of 1–2 m. Seepage flux and physical factors of the lake were uncorrelated. Even with a 3.2 m thick layer of gyttja, seepage influx was 13 ml m−2 min−1; therefore thick lacustrine sediments do not necessarily prevent inseepage. The results suggest that a local confined aquifer around and underneath the lake may cause the observed inseepage pattern.