Assessing habitat connectivity and distribution of organisms is essential to the understanding of population dynamics. Stable isotope ratio analysis is particularly useful in studying species connectivity and identifying potential nursing habitats. Isotope analysis of amphidromous organisms is a powerful tool to trace their movements, because they obligately migrate between salt- and freshwater habitats, often with their nursing time spending in nutrient-enriched estuaries. In this project we created C, N, and S isoscapes for the purpose of examining the habitat use in the estuaries by the aquatic organisms and, potentially, predicting the origins of mobile organisms. The isoscape graphs of the benthos showed spatial variation in δ¹³C and δ¹⁵N, and a significant change in δ³⁴S value at estuaries. Furthermore, isotopic data on mobile organisms suggest that isoscapes can potentially help to determine the origin and habitats of mobile shrimp organisms, while it may not be as useful in the context of fish species. Palaemon paucidens shrimp species most consistently had enriched and Caridina leucosticte -- most depleted in the heavier C, N, and S isotopes. This suggests that the more isotopically-enriched, and hence more marine influenced, Palaemon paucidens species have more recently migrated from the ocean to a more terrestrial habitat.