I created a model in modelbuilder and set the inputs to be parameters. When I open the model and the tool dialogue box shows up, the input files that I wish to select are not shown. These inputs are used for the "Select layer by location". Why is that and how do I fix it? I have all the input data set up in a geodatabase, and I can see it when I navigate to the .gdb in ArcCatalog.
You've said you're using Select Layer By.... This tool requires a layer as input. You said you've navigated to the data in ArcCatalog. ArcCatalog does not show layers, it shows the path to the data.
Use ArcMap, drag your data into the map, then open your tool. You should be able to chose the layer.