The COVID-19 pandemic has been a huge challenge for the Greek National Health System. Real-time reverse transcription PCR (rtRT-PCR) remains the reference method for early diagnosis, contact tracing, and containment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The aim of this study is the documentation of the epidemiological features of SARS-CoV-2 laboratory surveillance with rtRT-PCR in the population residing in the Pieria province of Greece. Of the 15,486 nasopharyngeal and oropharyngeal samples tested with real-time reverse transcription PCR for the presence of SARS-CoV-2 RNA, 8,051 (52%) were from females and 7,435 (48%) from males, aged 7 days–103 years, with 69.9% coming from the age group of >40 years. The 4,616 out of 15,486 (29.8%) samples came from hospitalised patients. There were 3,771 positive samples out of 15,486 (24.3%); 1,890 (50.8%) males and 1,881 (49.2%) females, with the age group of 40–59 years being dominant (29.9%). Those diagnosed for the first time made up 3,352 out of 3,771 (88.9%) of positive samples. The monthly positivity rate ranged from 6.24–15.69% during the B.1.1.7 variant wave, 17.38–52.89% during the B.1.617.2 variant wave, and 59.76% during the first month of the B.1.1.529 variant wave. Absence of detection of the spike protein gene target was observed in 1,371 (36.4%) of positive samples. Cycle threshold values <20, indicative of higher viral load, had 43.2% of positive samples during the B.1.1.7, 70.0% during the B.1.617, and 92.0% during the first month of the B.1.1.529 wave. The positivity and distribution of variants in the study population was in accordance with the respective results announced by official government authorities for the Pieria region.