Boeri Lake—a small (3.6 ha) but deep (39.6 m) crater lake on Morne Micotrin in Dominica, West Indies—presents a limnological enigma; it exhibits strong morphometric and circumstantial evidence for meromixis, yet it is not stratified. We tested the hypothesis that water seepage from Boeri Lake overcomes morphometric drivers of stratification and prevents the onset of meromixis. We compared water chemistry and plankton community composition in Boeri Lake to perennial streams on Morne Micotrin to assess if water discharging from these springs originates in Boeri Lake. Lacustrine phytoplankton and zooplankton taxa were detected in nearby streams, which also had similar water chemistry to Boeri Lake. In contrast, two other streams that drain Morne Micotrin and one neighboring reference stream had little in common with waters from Boeri Lake. This suggests that Boeri Lake’s anomalous limnology is explained by hydrologic connectivity to nearby flanking streams, and supports our hypothesis that subsurface water piping, combined with high annual rainfall, stymies the onset of meromixis. We provide an explanation for how holomictic lakes can persist and transport organisms through the ground in tropical mountain ecosystems and discuss implications of consistent water piping for plankton community assembly on island lakes.