Rare-earth doped upconversion nanocrystals have emerged as a novel class of luminescent probes for biomedical applications. The knowledge about their optical stability in aqueous solution under different pH and temperature conditions has not been comprehensively explored. Here we conduct a systematic investigation and report the emission stability and reversibility of typical NaYF4:Yb3+,Er3+ nanocrystals and their core-shell nanostructures in aqueous solution at different temperatures and with different pH values. These nanocrystals show reversible luminescence response to temperature changes, while low pH permanently quenches their luminescence. With the addition of inert shells, with thicknesses ranging from 1.5 nm to 8 nm, the emission stability and reversibility change significantly. Thicker inert shells not only lead to a significant enhancement in the emission intensity but also stabilize its optical responses which become less affected by temperature variations and pH conditions. This study suggests that upconversion nanocrystal-based sensitive temperature and pH sensors do not generally benefit from the core-shell structure usually recommended for enhanced upconversion luminescence.