This study explored the morpho-functional variations in the otoliths of Oreochromis niloticus (ON) and Chrysichthys nigrodigitatus (CN) across the Ikorodu (IKL) and Epe (EPL) regions in Nigeria's southern coastal lagoon system, with monthly sampling over twelve months. Digitized otoliths provided shape descriptors, and bathymetric analysis was conducted using the depth invariance index (DII). Remotely sensed reflectance (RSR) at 469 nm, 531 nm, and 555 nm assessed habitat productivity. Morpho-functional variations were evaluated using discriminant analysis (DA) and principal component analysis (PCA). Bathymetric analysis revealed that EPL has a deeper and more heterogeneous substratum than IKL. Additionally, Epe exhibited consistently higher RSR values than IKL. Sediment analysis showed higher clay and silt percentages in IKL and increased coarse sand in EPL, indicating distinct terrains. DA accuracy was high (ON: 92.0 %, CN: 90.8 % in cross-validation), highlighting variables such as area and circumference for ON and area, circularity, and compactness for CN. DA emphasized ellipticity, rectangularity, and roundness for ON, and form factor, compactness, circularity, and aspect ratio for CN. Higher reflectance values at EPL than at IKL indicate distinct ecological characteristics, with greater nutrient cycling and trophic productivity at EPL. Sediment analysis revealed distinct ecological heterogeneity and hydrological effects, with finer sediments in IKL indicating calmer conditions and EPL exhibiting higher energy conditions. Visualizing normal curve distributions for otolith shape descriptors in ON and CN populations revealed skewness patterns indicative of divergent adaptive features, possibly associated with habitat heterogeneity and productivity. The key otolith variables identified by DA and PCA suggest relative ecological opportunity and underscore the intricate relationships between otolith morphology and habitat variables (heterogeneity, productivity, sediment profile) in Nigeria's tropical southern lagoon system.