Decreased water quality in coastal environments due to land alterations by human activities has caused stressed and degraded coral reefs worldwide. The consequences of reduced water quality are not limited to coral reefs but also affect the quality of people’s lives by increasing the incidence of diseases, so areas highly impacted have been prioritized for management. The Guánica Bay Watershed Management Plan was developed to reduce the non-point sources of pollution that arrive at the bay and to protect adjacent coral reefs, however, 15 years have passed since its creation, and management actions have not been evaluated. This study aimed to assess the effectiveness of the management actions implemented in the Guánica Bay watershed. We described temporal trends (2002–2008 and 2016–2022) of remotely sensed diffuse attenuation coefficient at 490 nm (Kd490), a water clarity indicator, in one managed (Guánica Bay) and three non-managed (Guayanilla Bay, Descalabrado River, and Guanajibo River) estuaries in south and southwest Puerto Rico. This was achieved by integrating ocean-color satellite imagery from MERIS-Envisat and OLCI-Sentinel-3 sensors sampled using a beyond-Before-After-Control-Impact (beyond-BACI) approach. The analysis for the beyond-BACI found significant differences between periods (before and after) but the changes were unique to each location within the estuaries. The southern estuaries showed similar temporal trends, all having a peak in 2018 related to the passage of Hurricanes Irma and Maria and a trough in 2020 related to the Covid-19 pandemic. Kd490 did not decrease in Guánica after implementing management actions, suggesting that the impact of the hurricanes on water clarity probably outweighed the efforts made in the watershed to improve water quality. Further analysis should be done as new data is available and after the implementation of the last management actions suggested in the plan.