The occurrence of microplastics (MPs) in bottled water is still largely unexplored in Croatia. This study fills this gap by analysing six water brands available on the Croatian market, all bottled in either virgin or recycled polyethylene terephthalate (PET). In order to analyse microplastics down to a size of 1 µm, the water from the purchased bottles was filtered with silicon filters with a pore size of 1 µm and then micro-Raman spectroscopy was performed. A significant reduction in analysis time was achieved by using a randomly selected filter area of 12.05 mm instead of the conventional 100 mm. The results showed that polyethylene (PE), PET, and polyamide (PA) were found in all six brands and the blank. The highest detection frequency was found for PE (N = 19), followed by PET (N = 17) and PA (N = 14). Polyvinyl chloride (PVC) was found only in one brand, but in all three subsamples, packaged in recycled PET. By far the highest detection frequency of MPs occurred in the smallest fraction at a length < 5 µm. The highest number of MPs was for PET with 45% of the total amount, followed by PE (37%). Although MPs were identified in the blank water sample, the number was 12% of the total. Interestingly, the bottled water in virgin PET containers had more MPs than that in recycled PET. It should be noted that the purification system used to produce ultrapure water produced MPs, which poses an additional analytical challenge. The results should be considered as a snapshot and further monitoring is necessary to assess the extent of MP contamination of drinking water and to characterise the types of polymers and sources of the MPs. The current findings raise concerns about the presence of MPs in bottled water and warrant a thorough risk assessment to evaluate potential long-term health effects on humans.