Measuring bacterial growth potential (BGP) involves sample pre-treatment and inoculation, both of which may introduce contaminants in ultra-low nutrient water (e.g., remineralized RO permeate). Pasteurization pre-treatment may lead to denaturing of nutrients, and membrane filtration may leach/remove nutrients into/from water samples. Inoculating remineralized RO permeate samples with natural bacteria from conventional drinking water leads to undesired nutrient addition, which could be avoided by using the remineralized RO permeate itself as inoculum. Therefore, this study examined the effect of pasteurization and membrane filtration on the BGP of remineralized RO permeate. In addition, the possibility of using bacteria from remineralized RO permeate as inoculum was investigated by evaluating their ability to utilize organic carbon that is readily available (acetate, glucose) or complex (laminarin, gelatin, and natural dissolved organic carbon), as compared with bacteria from conventional drinking water. The results showed that membrane filtration pre-treatment increased (140-320%) the BGP of remineralized RO permeate despite the extensive soaking and flushing of filters (>350 h), whereas no effect was observed on the BGP of conventional drinking water owing to its high nutrient content. Pasteurization pre-treatment had insignificant effects on the BGP of both water types. Remineralized RO permeate bacteria showed limitations in utilizing complex organic carbon compared with bacteria from conventional drinking water. In conclusion, the BGP bioassay for ultra-low nutrient water (e.g., remineralized RO permeate) should consider pasteurization pre-treatment. However, an inoculum comprising bacteria from remineralized RO permeate is not recommended as the bacterial consortium was shown to be limited in terms of the compounds they could utilize for growth.