Subsurface and groundwater flow characterization is of great importance for various environmental applications, such as the dispersion of contaminants and their remediation. For single-hole flowmeter measurements, key characteristics, such as wellbore storage, skin factor heterogeneities, and variable pumping and aquifer flow rates, have a strong impact on the system characterization, whereas they are not fully considered in existing models and interpretation methods. In this study, we develop a new semi-analytical solution that considers all these characteristics in a physics-based consistent manner. We also present two new interpretation methods, the Double Flowmeter Test with Transient Flow rate (DFTTF) and the Transient Flow rate Flowmeter Test (TFFT), for interpreting data collected during single and multiple pumping tests, respectively. These solution and methods are used as follows. (i) The impact of wellbore storage, transient pumping rate, and property heterogeneities on the interpretation of data collected during single pumping tests are studied over 49 two-aquifer cases. (ii) The effect of the skin factor heterogeneity on transmissivity and storativity estimates, as well as the variability range of the (non-unique) corresponding solutions, are analyzed for the interpretation of multiple-pumping experiments. The results presented in this work show the importance of the various properties and processes that are considered, and the need for the new models and methods that are provided.