The mangroves experience seasonal flooding with high levels of sediment, and occasional extreme storms or very low rainfall due to El Niño effects.

The rivers carry large volumes of sediment and nutrients to the mangroves, depositing abundant sand and mud.

A study published in 2005 found mangroves stands consisting almost entirely of Laguncularia racemosa with many seedlings, which suggested that the forest was rejuvenating.

After the end of construction the mangroves began to repopulate bare inter-tidal zones, demonstrating their resilience.

[8] The woody stems of the mangroves provide habitats and food for marine fauna such as shellfish and fish.

Mammals that live in the trees include crab-eating raccoon (Procyon cancrivorus), mantled howler (Alouatta palliata), northern tamandua (Tamandua mexicana), raccoon (Procyon lotor), silky anteater (Cyclopes didactylus) and white-headed capuchin (Cebus capucinus).

[2] White-tailed deer (Odocoileus virginianus) are found in Avicennia bicolor and Laguncularia racemosa mangrove forests.

[9] Bird species include Amazon kingfisher (Chloroceryle amazona), grey-cowled wood rail (Aramides cajaneus), green kingfisher (Chloroceryle americana), lesser nighthawk (Chordeiles acutipennis), mangrove black hawk (Buteogallus anthracinus subtilis), roseate spoonbill (Platalea ajaja), rufous-browed peppershrike (Cyclarhis gujanensis), rufous-necked wood rail (Aramides axillaris) and yellow-billed cotinga (Carpodectes antoniae).

[2] In 2002 about 1,000 people worked in the near-shore artisanal fishery in the Gulf of San Miguel, often in the estuaries and mangrove channels.

[10] The new forestry regulations of 1994 made it illegal to harvest trees below a minimum trunk diameter, required environmental impact assessments for projects that could affect the mangroves, and banned expansion of aquaculture in mangrove areas while encouraging it on nearby salt pans.

[10] Large areas have been transformed into shrimp ponds, fields, cattle pastures and tidally flooded land.

Threats in Panama Bay also include land reclamation, urban growth, tourist facilities and pollution.