Methods and system for noninvasive determination of tissue analytes utilize tissue properties as reflected in key features of an analytical signal to improve measurement accuracy and precision. Physiological conditions such as changes in water distribution among tissue compartments lead to complex alterations in the measured analytical signal of skin, leading to a biased noninvasive analyte measurement. Changes in the tissue properties are detected by identifying key features in the analytical signal responsive to physiological variations. Conditions not conducive to the noninvasive measurement are detected. Noninvasive measurements that are biased by physiological changes in tissue are compensated. In an alternate embodiment, the analyte is measured indirectly based on natural physiological response of tissue to changes in analyte concentration. A system capable of such measurements is provided.