Avian influenza (AI) is a zoonotic disease significant to both public and animal health, caused by influenza virus A, and affects domestic poultry, wild birds, and mammals including humans. Aquatic birds are considered the natural reservoir of this virus. In 2016, Morocco experienced the first occurrence of low pathogenic H9N2 avian influenza virus (AIV) in poultry; however, no cases were reported in wild birds. The present study aimed to monitor the presence of AIV in wild birds in Morocco in order to trace the possible sources of the viruses affecting poultry. Between 2016 and 2019, 967 samples obtained from 480 birds representing 56 different wild bird species, 20 families, and 8 orders, mostly from Charadriiformes, Anseriformes, Pelecaniformes, and Passeriformes, were collected from various wetlands and relevant ornithologic sites in Morocco. These field samples consisted of 374 cloacal swabs, 321 tracheal swabs, 54 fecal samples, and 218 organ pools including the trachea, lung, liver, spleen, heart, intestine, and brain. The samples were examined for the presence of AIV using TaqMan-based real-time reverse transcriptase-PCR (rRT-PCR) targeting the matrix gene, followed by further subtyping rRT-PCR tests targeting the H1–H16 genes. The AI matrix gene was detected in 18 out of 967 samples (1.86%); positive samples were detected in 17 birds belonging to 10 bird species: two redshanks (Tringa totanus), one little stint (Calidris minuta), one ruddy turnstone (Arenaria interpres), one common snipe (Gallinago gallinago), one common greenshank (Tringa nebularia), one black-winged stilt (Himantopus himantopus), two black-headed gulls (Chroicocephalus ridibundus), one slender-billed gull (Chroicocephalus genei), six cattle egrets (Bubulcus ibis), and one Eurasian coot (Fulica atra). AIV was detected in 2 wetlands and 1 ornithologic site (Sidi Moussa Oualidia Complex, Smir lagoon and El Jadida Coast) and the highest positivity was revealed in fresh fecal samples (11.1%), indicating the suitability of this matrix for wild bird surveillance. Our results highlight that waders, gulls, and cattle egrets are the most affected species and may represent a potential risk for AI introduction in the poultry sector in Morocco. Regular monitoring of wild birds in Morocco, focusing in particular in the areas and species identified in this study as a high risk of virus circulation, should be implemented to anticipate and prevent possible AIV spread.