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I wish to select just the small green polygons (see image) and merge these with the pink polygon. However, I wish to leave the large green polygons that are over 1km2. However, all the green is one polygon, when I select one small area every green polygon is selected.

Any ideas?

See image

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you can use the processing tool "multiparts to singleparts" before: this will convert the multipolygon (the green one) into single polygons which you can join/merge afterwards.

enter image description here

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  • Thanks. There are over 500 small green patches are you aware of a fast way to merge them without clicking on them one by one? If I select an area with multiple qgis crashes?
    – Elise
    Feb 24 at 6:23
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After multipart to singlepart as @eurojam suggested, you may select all green areas smaller than 1 sqkm by pasting the expression $area<1000000 into the select by expression dialogue. Your green layer has to use a m-based CRS in order for this to work properly. You then may merge the selected green areas with the other layer as you see fit.

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