This study examined the effect of a water acidifier containing free and buffered short-chain fatty acids (SCFA-WA) on growth performance and microbiota of weaned piglets. In total, 192 male piglets, approximately 4 wk of age, were allocated to 24 pens (12 per treatment) with 8 piglets per pen. The piglets received either regular drinking water (negative control) or drinking water with the acidifier supplied at 2 L/1,000 L. Body weight and feed intake were measured weekly on pen level. During the first 2 wk, daily visual assessment and scoring of the feces was conducted. Fecal samples of three piglets per pen were collected on days 14 and 42 for high-throughput sequencing analysis of the microbiota. Piglets offered SCFA-WA had significantly improved feed efficiency in the third week (P = 0.025) and over the whole study period (days 0 to 42, P = 0.042) compared with piglets in the negative control group, with a strong tendency observed during the first feeding phase (days 0 to 21, P = 0.055). Furthermore, the water acidifier group had a higher water intake than piglets provided with control water during the second feeding phase (days 21 to 42, P = 0.028) and over the whole study period (days 0 to 42, P = 0.043). There was no significant difference in body weight, average daily gain, or average daily feed intake (days 0 to 21, 21 to 42, 0 to 42). Furthermore, there was no overall significant difference in fecal scoring between the treatments. In terms of the fecal microbiota response, piglets offered the water acidifier showed a significantly higher relative abundance (RA) of genus Clostridium sensu stricto 1 and a lower RA of genus Streptococcus compared to the control. Furthermore, the redundancy analysis showed a positive association between improved feed efficiency and daily weight gain and RA of Butyricicoccus and Faecalibacterium. In conclusion, consumption of the water acidifier containing free and buffered SCFA modulated the microbiota and improved feed efficiency in piglets.