Mangrove sediments serve as paleoenvironmental records of organic matter and nutrient accumulation. Ecuador, the world’s largest producer of whiteleg shrimp Penaeus vannamei in brackish waters, lost 43% of its continental mangroves between 1969 and 1999. Currently, more than 70,000 hectares of shrimp farms operate in estuaries with mangroves and within mangrove reserves. Variations in mangrove coverage and the extent of shrimp farms are described for the period 1996–2020 for two mangrove reserves, REMACAM and RVSMERM, with an observed increase in the extent of shrimp farms in both reserves. Four sediment cores obtained from mangrove drains and drains transformed into shrimp farm infrastructures were analyzed to observe the impact of this activity on the cumulative changes in total organic carbon (TOC) content and total nitrogen (TN) content, the fractionation of stable isotopes δ13C and δ15N, as well as the TOC/TN ratio. The mangrove drains in REMACAM had 3.8 times more TOC and 2.3 times more TN than drains transformed into shrimp farms in RVSMERM, with lower TOC/TN ratios. The organic matter in sediments from sectors with a higher proportion of shrimp farms mainly came from particulate organic matter of freshwater and freshwater algae compared to mangrove drains. Increases in TOC and TN content were recorded in all analyzed sectors, which could be attributed to the cumulative impact of population growth, the development of other agricultural crops, and continental deforestation, despite the fact that proportionally, the highest increases occurred in the sector with a greater influence of shrimp farms.