The reserve lies in one of the province's and of Cuba's most interesting regions in terms of physical geography, based on its natural history. Geologically, the primary influences are karstification, weathering and erosion.

The Canímar Formation distinguishes the area, and is exposed on the eastern bank of the River Canímar around 800 yards from the river mouth. The most characteristic locality accompanies the lower course of the river, between Antiguo Andarivel and the mouth. It dates from the Upper Pliocene and is mainly composed of clayey limestone of organic origin, fossil-bearing, of medium- to coarse-grained biocalcarenites and marls.

The sides of the canyon are steep, with gradients between 14% and 60%, declining to below 3% in the plateau area. The karstic forms found at the river mouth include dogtooth, potholes, small holes etc.

The River Canímar is one of the most typical and important antecedent rivers of the northern coast of Matanzas. Its rocky-banked mouth is some 400 yards wide. Depths in its delta reach 2.8 metres; upstream, in the interior, these reach 6 metres in the river's first meander. This makes it navigable as far as San José de Tumbadero, about 10 km from the river mouth, where it is joined by its tributary, the River Morat, which rises west-southwest of the Tetas de Camarioca heights and flows 20.2 km east-west to its mouth in the Canímar; it is navigable for about 1 km before that intersection.

Several karstic springs feed the Caímar. The remaining sources are basically rain and its network of tributary streams and rivulets.

Towards the mouth of the river (Canimar Abajo) the predominant species are laurel, fern, royal palm, trumpet tree, white mangrove, red mangrove, mutamba, sea hibiscus, almond, jack-in-the-bush, forest lilac, broom baccharis, coconut palm, guava and lemon. Vegetation covers 90% of the landscape.

The fruit trees that abound in the River Canímar area include the ackee, mamey sapote, plum, cherimoya, custard apple, soursop, star apple, sapodilla, avocado, orange, mango, lemon, grapefruit and eggfruit. Additional mamey sapote and almond trees have been planted. There has been some deforestation towards the livestock-breeding area (coverage declining to about 40%). The vegetation in the Las Carolinas area is more of the woodland type, notably bamboo in the bosque de galeria (tunnel wood).

Its fauna comprises bats and insects.

Aquatic species present a changing picture as one moves upstream from the river-mouth and its marine ecosystem (sardine, Madeiran sardinella, sea bass, sea bream, shad, manatee, lobster, shrimp, crab, black bream, horse mackerel, la plata croaker, silver dory, largehead hairtail, seahorse, moray eel, red snapper, lane snapper, trahira, French grunt, tanager, needle fish, grey mullet, trout, tench) towards the River Canímar and Las Carolinas freshwater ecosystem, although here too marine species penetrate with the tides (la plata croaker, grey mullet, flat head grey mullet, tanager, patao, sea bass, shad, shrimp, mostly in the River Canímar).

The denizens of the land comprise rabbit, deer, the Cuban hutia and hutia carabali.

Avian species include the trogon, woodpecker, hummingbird, thrush, rufous-and-white wren, mockingbird, Cuban grassquit, Cuban tody, Cuban blackbird, kestrel, owl, dove; and travelling towards the river-mouth, increasing numbers of gannet, gulls, rails, coot and anhinga.