With the onset of the coronavirus disease 2019 (COVID-19) pandemic, numerous countries imposed strict lockdown measures and travel bans, resulting in the closure of hotels. Over time, the opening of hotel units was gradually allowed, and new strict regulations and protocols were issued to ensure the hygiene and safety of swimming pools in the era of COVID-19. The present study aimed to evaluate the implementation of strict health COVID-19-related protocols in hotel units during the 2020 summer tourist season concerning microbiological hygiene and physicochemical parameters of water, and to compare the data with those from the 2019 tourist season. For this reason, 591 water samples from 62 swimming pools were analyzed, of which 381 samples were for the 2019 tourist season and 210 samples were for the 2020 tourist season. To examine the presence ofLegionella spp, 132 additional samples were taken from 14 pools, of which 49 in 2019 and 83 in 2020. In 2019, 2.89% (11/381) of the samples were out of legislative limits (0/250 mg/l) regarding the presence ofEscherichia coli(E. coli), 9.45% (36/381) were out of acceptable limits (0/250 mg/l) regarding the presence ofPseudomonas aeruginosa(P. aeruginosa) and 8.92% (34/381) had residual chlorine levels <0.4 mg/l. In 2020, 1.43% (3/210) of the samples were out of the legislative limits as regards the presence ofE. coli, 7.14% (15/210) were out of acceptable limits regarding the presence ofP. aeruginosaand 3.33% (7/210) of the samples measured residual chlorine levels <0.4 mg/l. The risk ratio (RR) in relation to the presence ofE. colidue to incorrect compliance with the requirements for residual chlorine was calculated for 2019 at 8.50, while in 2020 it was calculated at 14.50 (P=0.008). The RR of the presence ofP. aeruginosadue to inappropriate residual chlorine requirements was calculated in 2019 at 2.04 (P=0.0814), while in 2020 it was calculated at 2.07 (P=0.44). According to the microbiological hygiene and physicochemical parameters of the water samples studied, there was a significant improvement due to the strict protocols for the swimming pools in the summer season of 2020 compared to the tourist season of 2019, namely 72.72% (E. coli), 58.33% (P. aeruginosa), 79.41% (of residual chlorine <0.4 mg/l) in the three main parameters studied. Finally, an increased colonization byLegionella spp.detected in the internal networks of the hotels due to the non-operation of the hotels during the lockdown, the improper disinfection and stagnant water in the internal water supply networks. Specifically, in 2019, 95.92% (47/49) of the samples tested negative and 4.08% (2/49) tested positive (≥50 CFU/l) forLegionella spp., compared to 2020 where 91.57% (76/83) of the samples tested negative and 8.43% (7/83) tested positive.