Sympatric morphs provide valuable systems for studying incipient divergence despite incomplete reproductive isolation. In connected waterbodies with spatially heterogeneous habitats, one or more morphs may form metapopulation structures, generating eco-evolutionary dynamics unlike those in single lakes. We studied the phenotypic and genome-wide differentiation in Arctic charr (Salvelinus alpinus) in two Icelandic lakes: Thingvallavatn, known to harbour four distinct morphs, and a smaller downstream lake, Ulfljotsvatn. Our analyses confirm a single origin of charr polymorphism in this system, with all morphs present in both lakes. Relative morph abundances differ between the lakes: PL-charr dominate in Thingvallavatn, whereas LB-charr are most abundant in Ulfljotsvatn. Three morphs, large- (LB-), small (SB-) benthivorous and planktivorous (PL-) charr, are genetically distinct. The system likely forms a source-sink structure for both PL- and SB-charr, though migration rates from Thingvallavatn vary remarkably, resulting in distinct population dynamics. Conversely, LB-char exhibit genetic differentiation between the lakes, suggesting the presence of a separate population in Ulfljotsvatn. While piscivorous (PI-) charr appear genetically similar to PL-charr, evidence suggests hybridization between PI- and LB-charr in both lakes. Moreover, the higher hybridization in the downstream lake likely contributes to the observed erosion of genetic separation between LB- and PL-charr in Ulfljotsvatn. These findings suggest that the complex interplay of habitat heterogeneity and morph-specific migrations shapes the coexistence and eco-evolutionary dynamics of sympatric charr morphs in the connected lakes. Our study highlights the importance of investigating early divergence in spatially complex systems to advance eco-evolutionary research.