APPENDIX I List of sampling sites in the main river courses of Cyprus Island and the main geographical characteristics (Papastergiadou et al. 2008; Aguiar et al. 2013) Site Code Stream name Intercalibration type Latitude [ETRS89] Longitude [ETRS89] Altitude (m) Catchment (km2) Distance to source (km) Channel width (m) R-M5 34.8781187 33.337597 190 61.0 0.81 4 Prevailing channel substrate R-M5 34.8764458 33.339254 190 61.9 0.8 3 Gravel & Pebbles Cobbles CY_3 R-M5 34.8701073 33.342171 183 65.3 0.83 3 Cobbles CY_4 CY_5 R-M5 R-M5 34.8796961 34.9415787 33.334562 33.483295 202 135 56.1 91.2 0.81 0.38 2 4.5 CY_6 R-M5 34.9396979 33.486854 129 94.2 0.38 7 CY_7 R-M4 34.9273618 32.699559 430 67.0 0.82 6 Cobbles Cobbles Gravel & Pebbles Sand CY_8 R-M5 34.7628471 32.578831 83 205.0 1.17 25 Gravel R-M5 34.7959455 32.598537 133 184.0 1.14 15 Gravel CY_10 R-M5 34.8381705 32.646444 221 140.3 1.13 5 Cobbles CY_11 R-M5 34.854523 32.663604 254 118.9 1.14 6 CY_1 CY_2 CY_9 Syrkatis Treminthos Xeros Gravel Boulders & Cobbles Sand CY_12 R-M4 34.8885042 32.684893 367 98.1 0.82 6 CY_13 R-M4 34.889003 32.748005 435 115.6 0.75 35 CY_14 R-M5 34.7796346 32.671417 191 206.3 1 4 Gravel R-M5 34.7860354 32.687863 218 198.5 0.99 4 Gravel & Pebbles R-M5 34.7995984 32.706145 252 186.8 0.95 8 Sand CY_17 R-M5 34.6998584 32.561026 7 254.5 0.99 2 cobbles CY_18 R-M4 34.8872603 32.746894 434 115.7 0.77 50 Gravel CY_19 R-M5 34.7088859 32.563719 17 253.7 0.99 6 Cobbles CY_20 R-M5 34.749737 32.611893 103 241.0 0.99 5 Cobbles CY_21 R-M5 34.8639743 32.733005 380 124.6 0.75 4 Cobbles CY_22 R-M5 34.7852486 32.940212 275 115.0 1.21 4 Sand R-M5 34.7874425 32.945697 282 114.0 1.22 5 Sand R-M4 34.8284173 32.965585 392 91.8 1.09 2.5 Gravel CY_25 R-M4 34.8163329 32.963414 366 102.0 1.26 15 Gravel CY_26 R-M4 34.907254 32.991298 795 20.1 0.59 4 Sand CY_27 R-M5 34.7348546 32.678967 255 88.1 0.93 2 Gravel CY_28 R-M5 34.8233929 32.808513 620 25.4 0.52 3 Cobbles CY_29 R-M5 34.8033833 32.787197 550 38.0 0.52 1.5 Pebbles R-M5 34.8198354 33.311488 242 42.0 1.01 2 Gravel R-M5 34.8179196 33.241861 195 86.0 0.99 5 Gravel CY_15 CY_16 Diarizos CY_23 CY_24 Limnatis Xapotami CY_30 CY_31 Maroni Vasilikos Land Use Natural grassland Natural grassland Sclerophyllus vegetation Natural grassland Green urban areas Sclerophyllus vegetation Mixed forest Annual crops associated with permanent crops Sparsely vegetated areas Sclerophyllus vegetation Sclerophyllus vegetation Broad-leaved forest Broad-leaved forest Sclerophyllus vegetation Sclerophyllus vegetation Sclerophyllus vegetation Annual crops and Orchard Mixed forest Sclerophyllus vegetation Sclerophyllus vegetation Broad-leaved forest Fruit trees and berry plantations Fruit trees and berry plantations Green urban areas Fruit trees and berry plantations Sclerophyllus vegetation Annual crops associated with permanent crops Land principle occupied by agriculture with significant areas of natural vegetation Sclerophyllusvegetaion Sclerophyllus vegetation Sclerophyllus vegetation CY_32 R-M5 34.8423481 33.185647 371 27.8 0.82 7 Sand Sclerophyllus vegetation CY_33 R-M4 35.0369076 32.895253 396 62.0 1.3 9 Sand Green urban areas CY_34 R-M4 34.9689386 32.890115 896 10.1 0.88 5 Sand Mixed forest R-M4 34.9926026 32.903232 623 37.0 1.13 6 Cobbles Artificial CY_35 Kargotis R-M4 35.0028041 32.895713 558 43.8 1.16 3 Sand Land principle occupied by agriculture with significant areas of natural vegetation R-M5 35.0838225 32.71068 255 48.0 0.76 3 Sand Broad-leaved forest R-M5 35.0337101 32.698271 477 15.7 1.2 1 Sand Mixed forest R-M5 35.1093328 32.689028 200 38.0 0.87 5 Sand Mixed forest R-M5 35.1023991 32.668799 270 30.6 0.99 3 Sand Mixed forest R-M5 35.0660142 33.019599 290 81.0 0.94 2 Sand Green urban areas CY_42 R-M5 34.957249 32.507248 185 78.0 0.92 2 Gravel Mixed forest CY_43 R-M5 35.0023804 32.434726 51 178.0 1.06 8 Cobbles CY_44 R-M5 34.9585847 32.534984 242 60.0 0.84 2 Gravel CY_45 R-M5 34.985452 32.555442 336 30.2 1.01 3 Sand Mixed forest CY_46 R-M5 34.9413603 32.611671 430 41.0 0.92 3 Gravel Mixed forest CY_47 R-M5 34.9480266 32.618112 459 39.4 0.61 5 Boulders Mixed forest R-M5 34.8451273 32.54468 204 123.7 0.92 4 Cobbles Broad-leaved forest CY_49 R-M5 34.81244 32.528492 157 180.0 0.98 7 Cobbles Fruit trees and berry plantations CY_50 R-M5 34.8394093 32.544427 197 131.1 0.92 3 Cobbles Broad-leaved forest CY_51 R-M5 34.8359652 32.542193 191 132.0 0.92 3.5 Pebbles Sclerophyllus vegetation R-M5 34.768358 33.101139 100 110.0 0.66 8 Gravel Constraction site R-M5 34.777058 33.103739 121 108.0 0.99 4 Sand Sclerophyllus vegetation R-M4 34.8405975 33.113149 351 72.9 0.71 2.5 Cobbles Broad-leaved forest R-M5 34.7804619 32.856057 380 39.7 1.54 12 Cobbles Mixed forest 3 Cobbles/ Pebbles Water course Sand Land principle occupied by agriculture with significant areas of natural vegetation CY_36 CY_37 Limnitis CY_38 CY_39 Pyrgos CY_40 CY_41 Elias Chrysohou CY_48 Ezousa CY_52 CY_53 Germasogeia CY_54 CY_55 Kryos R-M4 CY_56 34.9877909 32.825662 713 15.6 0.64 Fruit trees and berry plantations Land principle occupied by agriculture with significant areas of natural vegetation Setrachis CY_57 R-M4 35.0002551 32.827137 582 23.0 0.93 6 2 APPENDIX II Summary of the main pressures in the study area that were included in the CCA (MED GIG criteria, Aguiar et al. 2013) modified from Gomez et al. 2005) Pressures 1. 2. 3. 4. 5. 6. 7. Channel profile / cross section alteration Degree of channel profile modification present at the site/cross section alteration Channel morphology Degree of the morphological modification of the channel present at the site Local habitat alteration Stream hydrology Upstream dams influence Water abstraction Dykes (flood protection) 8. Land use type 9. 10. Description Alteration of in stream habitats Degree of the hydrological alteration present at the site Impacts Elimination of riparian vegetation (1-7, 9,10) Alteration of hydrological processes (1,2,4,5,6,7) Habitat destruction (1,2,3,7,9,10) Introduction of foreign species (9,10) Eutrophication (4,9,10) Effect of upstream dams Effect of water abstraction at the site Effect of dikes for flood protection CORINE land cover or verbal description of land use in immediate vicinity of site Urbanization Urban and industrial areas in immediate vicinity of site Agriculture Agriculture at the immediate vicinity of site Surface and groundwater pollution (9,10) Channel desiccation (1,2,5,7) Changes in aquatic communities (3,4,5,6) Replacement of natural plant communities by weed species (1,2,9,10) Eutrophication, Water quantity & quality (3,6,10) APPENDIX III Dendrogram derived from the UPGMA clustering for the investigated a) permanent river R-M4 sites (1: Community Type I, 2: Community Type II, 3: Community Type III) and b) temporary river R-M5 sites (1: Community Subtype Ia, 2: Community Subtype Ib, 3: Community Type II). The abbreviations of the sampling sites are the same as in APPENDIX I. 4 APPENDIX IV Inter set correlations between water quality parameters and the geomorphologic/ human pressures descriptors, and the three Axes of the CCA at R-M4 and R-M5 sites. Water chemistry Eigenvalues Spp-Env corr. pH Conductivity Alkalinity Ammonium Nitrate TN TP Phosphate DO Human pressures Axis 1 0.817 P=0.5 0.965 P=0.71 -0.404 0.013 0.209 0.101 -0.097 -0.062 0.36 0.043 0.124 Axis 1 0.891 Eigen values P=0.04 0.987 Spp-Env corr. P=0.24 Channel cross alteration -0.061 Channel morphology -0.11 Habitat alteration -0.197 Stream hydrology -0.085 Dam influence N/A Water abstraction -0.595 Dykes -0.082 Land_Use -0.198 Urbanization 0.278 Agricultures -0.544 R-M4 Axis 2 0.773 Axis 3 0.47 0.963 0.971 0.025 -0.664 0.13 0.071 -0.577 -0.55 0.027 -0.252 0.184 R-M4 Axis 2 0.763 Axis 3 0.513 0.982 0.902 -0.505 -0.651 -0.746 -0.288 N/A -0.231 -0.271 -0.576 -0.324 0.089 -0.064 0.241 0.342 0.125 -0.007 0.037 0.144 0.099 -0.542 -0.378 -0.104 -0.224 0.384 N/A 0.473 0.402 -0.64 -0.127 0.283 Axis 1 0.37 P=0.27 0.914 P=0.84 0.215 -0.753 0.067 0.138 -0.465 -0.461 0.041 0.192 0.052 Axis 1 0.317 P=0.83 0.927 P=0.67 -0.519 -0.049 0.106 -0.669 -0.751 -0.545 0.142 0.283 0.059 -0.586 R-M5 Axis 2 0.31 Axis 3 0.27 0.925 0.902 0.085 -0.324 -0.476 0.058 0.509 0.521 0.017 0.239 -0.41 R-M5 Axis 2 0.288 Axis 3 0.258 0.942 0.88 0.14 -0.023 -0.477 -0.275 -0.254 0.234 0.063 -0.372 -0.368 0.261 -0.025 0.174 0.354 0.213 0.35 0.364 -0.036 0.257 0.251 0.155 0.085 0.539 -0.106 0.221 0.43 0.412 0.208 -0.027 0.023 5