Metapenaeus moyebi, a lacustrine penaeid shrimp exhibiting complete estuarine residency, constitutes a major component of tropical lagoon shrimp fisheries. This study provides the first comprehensive population assessment of the species in Sri Lankan waters, based on monthly sampling of 4,200 individuals from the Jaffna Lagoon between January 2022 and January 2025. Population parameters were estimated using TropFishR, and length at 50% sexual maturity (L_m₅₀) was analyzed using SizeMat. Spatial and temporal patterns were examined through distributional and phenological analyses. The von Bertalanffy growth parameters were estimated as L∞ = 11.2 cm, K = 2.64 yr⁻¹, and t_anchor = 0.18 yr. Estimated fishing mortality (F = 7.54 yr⁻¹), was below the maximum exploitation threshold (F_max = 8.91 yr⁻¹), with F/F_max = 0.73. However, ratios relative to conservative reference points, F/F_0.5 (2.64) and F/F_0.1 (1.71) exceeded 1, indicating potential sustainability concerns. Length at 50% and 75% capture (L_c50 = 5.98 cm, L_c75 = 6.27 cm) were smaller than L_m₅₀ (7.4 cm), suggesting growth overfishing due to harvest of individuals before sexual maturity. Reproductive phenology showed peak maturity of females (94%) by November, indicative of the spawning season, while immature individuals dominated catches from March to May, reflecting the main recruitment period into the lagoon population. Spatial analysis revealed significant ontogenetic segregation (p < 0.05), with immature shrimp concentrated near the lagoon mouth (52%) and decreasing toward inner lagoon zones. These findings demonstrate that M. moyebi maintains a resident life cycle with distinct spatial and temporal population structuring. Sustainable management requires spatially explicit conservation measures, including protection of nursery habitats and seasonal harvest closures to maintain stock resilience.