RPSB NI said that voting to leave would lead to uncertainty over the protection of important sites.
The charity also claimed that EU agreements had been key to protecting birds and habitats.
The comments were made as part of a written submission to a parliamentary inquiry.
The Northern Ireland Affairs Committee at Westminster are conducting an inquiry into the impact of the EU referendum in Northern Ireland.
As part of their submission, RSPB NI said if the UK voted to leave, EU protections for species and habitats would "no longer mandatorily apply".
The charity claimed the EU had had a "positive impact" in other areas such as air and water quality and renewable energy targets.
It said international agreements on nature conservation and robust enforcement, were key to protecting birds and habitats.
Although RSPB NI said they have issues with certain aspects of the Common Agricultural Policy, the potential loss of agri-environment schemes within it - which pay farmers to conserve wildlife - would be "a concern".
The charity also questioned whether a Brexit would affect cross border habitat improvement schemes which attract EU funding.
A leading wildlife charity in Northern Ireland has said leaving the EU would have significant implications on its work.