Are you specific on what macrophytes you want to monitor? If yes then I suggest that you choose one large water body like a lake, divide it into transects then carry out the sampling. In this case, depending on the question you have, you will have to sample the inlets and outlets. Replicate the same process in other lakes then compare the results.

How cheap or expensive the project will cost is highly dependant on the scientific questions you are seeking to answer because they determine the methodology as well.

There are macrophytes that like still water like the lake and those that are in rivers. So I think there is no harm in studying them as they also contribute to understanding ecological health of the water body.

I think monitoring macrophytes in rivers is relatively cheap compared to the macro-invertebrates, benthic algae and fish. In theory macrophytes can be used in rivers, but macro-invertebrates or benthic algae are much more "reliable", due to the large number of species compared to macrophytes. I have tried to reproduce many of the results from TI (Trophic Indices), but fail to do so (my first attempt https://www.researchgate.net/post/Influencing_factors_of_aquatic_plants_why_not_dissolved_organic_carbon_or_sediment_nutrients). In lakes the use of macrophytes seems to yield higher correlations as in rivers, but consider the critique of the first two articles below. The variability of many macrophytes along the trophic gradients is also huge (I mean huge). Yet, we can use them assess water quality and many more factors, but not based on the methods we employ and expectations we have of them (This seems to work(?) https://www.researchgate.net/post/Is_it_possible_estimating_environmental_conditions_with_a_Bayesian_approach). The references below give an nice overview of the issues.

Article River macrophyte indices: Not the Holy Grail!

Article Distribution of aquatic macrophytes in contrasting river sys...

Article The aquatic macrophytes of an English lowland river system: ...

https://link.springer.com/article/10.1007/s10750-021-04516-x?utm_source=toc&utm_medium=email&utm_campaign=toc_10750_848_5&utm_content=etoc_springer_20210223

https://link.springer.com/article/10.1007%2Fs10661-017-6368-6

https://link.springer.com/article/10.1007/s10750-006-0101-8

Yes, the native macrophytes

I think macrophytes are important in aquatic ecosystems and relativeča cheap to monitor

There are expensive (labor intensive and cost) and relatively inexpensive ways to monitor macrophytes. Decide what your goals are, and also which cost needs to be minimized (labor versus monetary). Most groups oversample compared to the goal.

https://www.ser.org/news/565466/SER-RM-Workshop-Practical-Tools-and-Sample-Designs-for-Ecological-Restoration-Monitoring.htm

There is some useful info in the first talk of that workshop, especially in the q&a.

The use of macrophytes in monitoring is not particularly expensive. The choice depends on the goals set, as already written above.

Macrophytes are rarely used in river monitoring because they are fairly rare in flowing water. All of the erosion and deposition in active river channels tends to inhibit their growth.

Macrophytes are used in monitoring in many countries in rivers, densely vegetated with macrophytes. They are absent in rivers in mountain regions, where the substrate is not suitable.

Macrophytes are being monitored in both rivers and lakes in many EU countries that implement the Water Framework Directive. They are used as indicators of ecological status as they can reflect changes in the hydromorphology and nutrient content of lotic and lentic environments and are quite cheap to sample in streams and wadeable rivers.

Please note that macrophytes are a broad group of aquatic plants including not only angiosperms but also bryophytes, macroalgae and aquatic ferns. In high and mid-altitude streams rooted angiosperms are rare but bryophytes, ferns and charophytes are not uncommon. In lowland slow-flowing rivers, rooted or free-floating plants are usually more abundant and can form dense populations.

agree!