Great that you got the results.
Regarding the noise, CHL results for S2 MSI is more noisy than S2 OLCI this is known.
Reasons might be that S2 has been desgined with land application in mind and OLCI was desgined for land and ocean. The signal to noise ratio is probably not so good for water areas. The higher resolution might be also a cause. The noise is smoothed out when creating L3 images. You can smooth your generated image by using the filters provided in SNAP without creaing L3 images. This should result in nicer looking images.
But maybe I’m talking rubbish. Take my comments with a grain of salt. Even I have learned a few things the last years, I’m still a software developer in the first place and not an EO scientist.
Maybe @abruescas can comment and correct me or add additional information.