Coastal lagoons and estuaries provide critical ecosystem goods and services to society and the majority of the world’s population live in coastal regions (Bianchi et al. 1999; Bianchi 2007; McGranahan et al. 2007; Michael and Paerl 2010). However, population growth, land and water use alteration, and habitat fragmentation in connecting coastal watersheds reduce the productivity and health of the coastal environment (Day et al. 2007; Borja et al. 2008). A detailed analysis of coastal systems, ecological dynamics, and carrying capacity is needed to avoid further ecological damage that would endanger human economic and functional dependence on these valuable ecosystems (Borja and Dauer 2008). Understanding the ecogeomorphology and biogeochemistry of coastal regions requires the consideration of humans as agents of change (Borja et al. 2008; Hopkinson et al. 2008; Bauer et al. 2013). The Mexican coastal zone encompasses complex geomorphological settings along a 11,600 km coastline (RiveraArriaga and Villalobos 2001) that interacts with a wide continental shelf (500,000 km), particularly in the Gulf of Mexico (Rivera-Arriaga and Villalobos 2001; Yanez-Arancibia and Day 2004b; Yanez-Arancibia et al. 2013) and the Gulf of California (Lluch-Cota et al. 2007). Landforms along both the Pacific and Gulf of Mexico coasts are widely diverse due to their geological history and include reef coasts, sedimentary basins, karstic environments, and volcanic/tectonic rocky coasts (Seingier et al. 2011). Despite Mexico’s extensive area of estuaries (16,000 km) and coastal lagoons (12,500 km) (Ortiz-Lozano et al. 2005), there is limited information about the hydrology and hydrodynamic patterns of these systems, including changes associated with human activities (Rivera-Arriaga and Villalobos 2001). Major human activities altering coastal hydrological patterns in Mexico include road construction, urban development, coastal tourism, and oil and gas exploration (Ruiz-Luna and BerlangaRobles 2003; Murray 2007; Vidal and Filograsso 2008). These alterations may lead to increased water residence times that exacerbate eutrophic conditions in coastal waters already affected by agricultural activities (i.e., fertilizers) and untreated sewage loads (e.g., Paez-Osuna et al. 1998; Ahrens et al. 2008). The sustainability of economic development in Mexican coastal regions is strongly affected by extensive watersheds, particularly in the Gulf of Mexico (Lozano et al. 2000; Sanchez-Gil et al. 2004; Cruz and McLaughlin 2008; YanezArancibia et al. 2013), where discharge from the four largest rivers in the country (Grijalva-Usumacinta, Papaloapan, Coatzacoalcos, and Panuco; total discharge 208,621× 10 m year) (NWCM-CONAGUA 2008) delivers sediment and nutrients that control coastal productivity (e.g., fisheries and aquaculture) (Espinoza-Tenorio et al. 2011) and supports hydroelectric power generation (NWCMCONAGUA 2008). Riverine discharge subjects estuarine and coastal areas to nutrient enrichment and hydrocarbon and pesticide pollution from surface water runoff, atmospheric deposition, and groundwater discharges (Delgado-Gonzalez et al. 2011). The Mexican coastline plays a critical role in the country’s economy. However, it is not clear what the net response of these coastal ecosystems will be to multiple stressors, from human caused perturbations (e.g., land use, nutrient enrichment, and pollution) (Sanchez-Gil et al. 2004; Communicated by Iris C. Anderson and Wayne S. Gardner