Clip Categorized Polygon with another Polygon

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Ok, so first off, I've gone through the forum, and looked at every post that sounds similar. They have all been solved, but none of the solutions have worked for me.

Basically, I have created a contoured polygon layer from a set of csv points. My polygon layer looks like this:

Now, the issue is that over the water I don't actually have data, that area is being filled in by the contour plugin. So, I have two options the way I see it:

1) Create contours that do not interpolate over missing stretches of data; OR

2) Clip this contour layer with a polygon so it only displays my actual dataset.

Below you can see my contour layer with the 'mask' of where my data should actually exist:



I have tried clipping, using the intersect tool, using the digitize tool etc. to just clip this layer, but I'm obviously doing something wrong. More times than not the tools just take one of the categories from the contour layer and ignoring the other two. Like this:



I have tried saving all my layers as new shapefiles in the same CRS. I have also gone through and checked the geometry for errors and fized them where applicable. Any thought on how I can accomplish what I'm trying to do?

Thanks!



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