Giardia and Cryptosporidium are the most frequent enteric protozoa causing gastroenteritis in humans worldwide. Intense recreational activity at Portuguese river beaches triggered the opportunity for a 2-year seasonal survey of 19 large river basin beaches. A total of 74 samples were collected and processed according to USEPA Method 1623 to detect Cryptosporidium and Giardia (oo)cysts. Faecal indicators (thermotolerant/total coliforms, Escherichia coli, and enterococci) and physicochemical parameters were also analysed according to the EU Bath Water Directive (BWD). Results pointed to a widespread presence of these protozoa at Portuguese river beaches. The percentage of samples testing positive for Giardia and Cryptosporidium were 85 and 82% respectively, with no significant differences between wet and dry seasons (p > 0.05). Although Portuguese river beaches present a very low exposure risk for infection with Giardia and Cryptosporidium (under 10−3), a few particular cases revealed values over 0.2%, and were related to stormy wet events. The correlation between levels of Giardia and thermotolerant coliforms, E. coli and enterococci, was high (r ≥ 0.87, p < 0.001), suggesting the need to carry out specific procedures for the detection of Giardia and Cryptosporidium whenever the values of those faecal indicators approach the maximum allowed level of the EU BWD.