Hydrologic data were collected in the nearshore lake-bottom sediments of five lakes on western Cape Cod, Massachusetts: Ashumet (Falmouth), Long (Centerville), Santuit (Mashpee), Shubael (Barnstable), and Snake (Sandwich) Ponds. Water budgets of flow-through glacial kettle lakes are commonly dominated by groundwater flow into and surface-water seepage out of the lake, and inputs and losses from precipitation and evaporation are typically smaller. This data release presents water flux data collected from sites at the five lakes where lake water is seeping downward across the groundwater/surface-water interface into the groundwater system. Detailed characterization of water flux across the lake-bottom interface is critical to assessing the lake's influence on the groundwater system. The water fluxes were calculated for four of the lakes by using measurements of bottom-sediment temperature in shallow (less than 20 centimeters) vertical profiles and were measured directly at all five lakes by using seepage meters.
 
 Data were collected over four periods. Seepage meter measurements were made during August and September 2015. Temperature profile data were collected from July 27 to October 13, 2016; September 19 to October 11, 2017; and February 13 to February 23, 2018.
 
 The data are divided into four data sets (child items): (01) Temperature measurements from the vertical profiles, (02) calculated seepage rates from the temperature profiles, (03) measured seepage rates from the seepage meters and associated site information, and (04) average calculated seepage rates for each vertical temperature profile site and associated site information.